Alpha Natural Resources was fined $27.5 million and agreed to spend $200 million more to reduce discharges of polluted water from its coal operations into waterways across five Appalachian states.
It's the largest fine for such violations in the history of the federal Environmental Protection Agency, which proposed the settlement Wednesday.
Virginia-based Alpha was cited for violating water pollution permits more than 6,000 times between 2006 and 2013. Some of the discharges continue to this day across Pennsylvania, Kentucky, Tennessee, Virginia and West Virginia, according to officials. Many of the violations stemmed from Alpha's two longwall mine complexes in Greene County: Emerald Coal and Cumberland Coal Resources.
The government says Alpha and its 62 subsidiaries discharged heavy metals and other contaminants harmful to fish and other wildlife from nearly 800 outfall pipes directly into rivers, streams and tributaries, according to the government.
The polluted water is a by-product of washing and treating coal.
"The state agencies should be made responsible for this," said Aimee Erickson, executive director of the Bridgeville-based environmental advocacy group Citizens Coal Council. "If they were doing their job, this should never happen."
Ms. Erickson's group, which is suing Alpha for the same violations, discovered the company was exceeding its permit limits by reviewing quarterly monitoring reports that Alpha had to file with the Pennsylvania Department of Environmental Protection.
In 2010, Citizens Coal Council took the information to federal regulators and handed over 72,000 pages of documents showing the company regularly discharged more than it was allowed, according to its own measurements.
According to EPA records, processed water from Alpha's Emerald coal mine in Greene County was discharged into creeks and tributaries to the Monongahela River. Some of these are impaired waters, others warm water fisheries.
At Cumberland, discharges of manganese, total suspended solids and iron into Whitely Creek were consistently above what was allowed, sometimes 10 times more.
Gene Kitts, senior vice president of environmental affairs at Alpha, said the company has been improving its track record. In 2012, it exceeded its Pennsylvania permit levels 726 times between Cumberland, Emerald, and Amfire Mining Co., an Alpha subsidiary that operates underground and surface mines in the state. In 2013, the number dropped to 294.
"I'm not saying 294 is good," Mr. Kitts said. "We're not satisfied with 294 by any means. But overall in Pennsylvania, that 59.5 percent improvement was a good start towards cutting it down to something that is much more acceptable, much more manageable."
For certain pollutants, Mr. Kitts said, the discharge limits are too low and the company plans to work to raise them, as in the case of selenium and aluminum.
At the same time, Alpha will be installing passive treatment systems to minimize its selenium discharges and, by September 2016, the consent decree requires the company to build an advanced nanofiltration plant to treat metals coming from its Emerald and Cumberland complexes.
Mr. Kitts said he did not believe the company caused "significant adverse harm to the streams or to the aquatic life in those streams."
"Most of these were relatively isolated exceedances," he said.
The $27.5 million fine represents a landmark for the EPA, according to Cynthia Giles, head of the EPA's enforcement office.
"It's the biggest case for permit violations, for numbers of violations and size of the penalty, which reflects the seriousness of violations,'' she said.
The Pennsylvania DEP will get $4.125 million of the penalty, which will be deposited into its clean water fund.
The deal has been in the works for years, said Amanda Witman, a spokeswoman for the agency who could not say when the agency discovered the violations or how the company was penalized until now.
"In our experience it is always more beneficial to negotiate these types of things," Ms. Witman said. "Often times, industry is more willing to work with us and more willing to comply with regulations when they don't see us as the hammer that's going to come down on you."
From 2006 to 2013, the EPA documented at least 6,289 Alpha violations of permit limits for pollutants including iron, aluminum, selenium and manganese, according to court papers.
Most violations stemmed from the company's failure to operate existing treatment systems properly, install adequate ones and implement appropriate water handling and management plans, prosecutors said.
Under the agreement, the mine operators will install wastewater treatment systems and take other measures aimed at reducing discharges from 79 active coal mines and 25 coal-processing plants in those five states.
According to the company's annual filing with the Securities and Exchange Commission, Alpha is involved in at least a dozen lawsuits over its water discharges.
The company acquired Massey Energy in 2011, and more than half of the violations covered by the new settlement stemmed from that company's operations. Massey was fined $20 million in 2008 by the federal government for similar violations of water pollution laws.